[gmx-users] Re,i don't know how can i determine emtol

[Ivan Gladich]

On 11/22/2012 09:32 PM, Ali Alizadeh wrote:
>
> 1- In your opinion, Can i simulate that system?
>>>> In my (humble) opinion:
>>>>
>>>> 1)Of course you can simulate that system...however  I doubt that, without
>>>> starting from the exact initial configuration with the exactly same
>>>> set-up,
>>>> you can get the same results (i.e. see the nucleation).
>>>> The onset of ice nucleation is a random process and requires very long
>>>> simulation (the paper that you posted was analysing micro-second
>>>> trajectories!!).
>>>> There is the risk that you could try several different initial
>>>> configurations at several temperature without getting anything.
>>>>    However, read carefully that paper, I do not remember all the details.
>>>>
>>>> If you are interested in ice crystal growth, I would suggest to start
>>>> with
>>>> an initial water/ice system: at temperature below the melting one you
>>>> will
>>>> see formation of new ice starting from the initial ice matrix.
>>> I do not know how  can ice crystal in initial step, i study papers and
>>> i know ice , crystals formation and dissociation of crystals is very
>>> difficult,
>>> and we can use this method(as you said above) for melting or
>>> freezing(if i say correct)
>>>
>>> My problem is this case, how can i have a crystal in initial step,
>>>
>>>
>> You have three options
>>
>> 1) Surfing the web searching for some structure.
>>
>> 2)Try to implement the proton disordering algorithm of Buch et al.,
>> (V. Buch, P. Sandler and J. Sadlej, J. Phys. Chem. B, 1998, 102,
>> 8641–8653)
>>   which specifies orientations of water molecules such that ice
>> Ih Bernal–Fowler constraints for each molecule are satisfied.
>> (J. D. Bernal and R. H. Fowler, J. Chem. Phys., 1933, 1, 515–548)
>>
>> 3) Someone kindly offer you his own structure, e.g.
>>
>> http://marge.uochb.cas.cz/~gladich/Teaching.html
> That's right,
>
> Is it possible that i know how can you construct it?
> You use TIP5P, and i do not know your force field?
>
> In fact i should  construct this structure by self,
> Can you give some advices so that i can construct it?
>
>
I constructed the structure using the method 2) with the Buch's algorithm.
Concerning TIP5P and TIP5P-Ew, here below the references:

1) Mahoney and Jorgensen, J. Chem. Phys., 2000, VOLUME 112, NUMBER 20
2) S. W. Rick, J. Chem. Phys., 2004, 120, 6085–6093.

All the best
Ivan

-- 
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Ivan Gladich, Ph.D.
Postdoctoral Fellow
Academy of Sciences of the Czech Republic
Institute of Organic Chemistry and Biochemistry AS CR, v.v.i.
Flemingovo nám. 2.
166 10 Praha 6
Czech Republic

Tel: +420775504164
e-mail: ivan.gladich at uochb.cas.cz
web page:http://www.molecular.cz/~gladich/
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